I pay a fixed rate up-front for reprint rights, which is a one-time deal. This is mostly because pro rata royalties on an anthology are a pain (I've done this before, it involves sending out lots of tiny single-digit-dollar checks), but also because it's unlikely for me to make back the money I spend on anthology creation (science fiction short stories are a tiny market).
This is a hobby project for me, I'm obsessed with trying to get more people to read science fiction short stories. I spent about $6k creating the anthology (to pay for cover art, reprint rights, proof prints, etc), and I'll probably recoup about half of what I spent? We'll see, I'm currently testing various marketing strategies.